## [1] "O77_p4_IFNg_R1_2.hicup.bam"

Truncation & Mapping

Truncation Frequency

Category Read 1 Read 2
Total 61,280,185 61,280,185
Not Truncated 34,964,752 35,780,238
Truncated 26,315,433 25,499,947

Truncated Read Length

Category Read 1 Read 2
Average Length Truncated 44.5 43.7

Mapping Efficiency

Category Read 1 Read 2
Too Short To Map 5,433,918 5,719,737
Unique Alignments 50,413,656 48,288,169
Multiple Alignments 1,985,585 1,786,075
Failed To Align 3,447,026 5,486,204
Paired 40,683,842 40,683,842

Truncation and Mapping Bar Plot

Filtering

Filtering Breakdown by Category

Category Count
Valid Pairs 14,951,895
Invalid Pairs 25,731,947
Same Circularised 45,474
Same Dangling Ends 2,663,670
Same Fragment Internal 10,168,912
Re Ligation 10,950,829
Contiguous Sequence 715,129
Wrong Size 1,187,933
Total Pairs 40,683,842

Filtering Breakdown Pie Chart

Ditag Length Distribution

Frequency Line Plot

Deduplication

Deduplication Summary Table

Category All Ditags Unique Ditags
Read Pairs 14,951,895 29,624
Cis-close (<10Kbp) 1,538,070 2,815
Cis-far (>10Kbp) 8,658,523 15,825
Trans 4,755,302 10,984

Deduplication Bar Chart

Analysis produced by HiCUP - a tool for mapping and performing quality control on Hi-C data

Babraham Bioinformatics